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1 Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan
2 Laboratory of Microbiology and Immunology, Graduate School of Health Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
Correspondence
Tsuyoshi Kenri
kenri{at}nih.go.jp
| ABSTRACT |
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Present address: Pharmaceuticals and Medical Devices Agency, 3-3-2 Kasumigaseki, Chiyoda-ku, Tokyo 100-0013, Japan.
Two supplementary tables, listing the oligonucleotides used in this study, are available with the online version of this paper.
| INTRODUCTION |
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Mycoplasma penetrans was first isolated from a urine sample of a human immunodeficiency virus (HIV)-infected patient (Lo et al., 1992
). It was also isolated as a potential aetiological agent from a primary antiphospholipid syndrome patient without HIV infection (Yáñez et al., 1999
). Although the pathogenicity of M. penetrans to humans remains questionable, the characteristics of this bacterium (i.e. invasion of eukaryotic cells, toxicity to chick embryo, and haemolytic and haemoxidative activity) (Girón et al., 1996
; Kannan & Baseman, 2000
; Lo et al., 1993
) suggest its potential pathogenicity to humans. M. penetrans also has the ability to change its surface antigenicity frequently by changing the expression pattern of the P35 family lipoproteins (Neyrolles et al., 1999
; Röske et al., 2001
). The P35 family lipoproteins are encoded by the mpl genes and, thus far, 38 mpl genes have been found in the M. penetrans HF-2 genome. Of these 38 genes, 30 form a large gene cluster in a 50 kb region of the genome (Horino et al., 2003
; Sasaki et al., 2002
). M. penetrans uses a unique mechanism to modulate the expression of these mpl genes. Most of the mpl genes have an independent promoter for their expression. These promoter sequences are present in approximately 135 bp DNA regions and are flanked by 12 bp inverted repeats (IRs). Inversion of these promoters causes ON/OFF switching of individual mpl genes. The invertible promoter elements also contain unique sequences that form a terminator-like structure depending on the direction of promoters (see Fig. 4a
). This terminator-like structure may serve to prevent readthrough transcription from preceding genes or antisense transcription from OFF configuration promoters (Horino et al., 2003
). Thus, the mpl genes have unique genetic switches, which possess promoter and terminator functions in the short DNA region. To further characterize these unique genetic switches and understand the nature of antigenic variation of M. penetrans, in this study we attempted to identify the factors involved in mpl gene promoter inversions. For this purpose, we reconstructed the mpl promoter inversion system in Mycoplasma pneumoniae and Escherichia coli cells.
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| METHODS |
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Cloning of the p42 and p35 promoter regions.
PCR primers used for cloning are listed in Supplementary Table S1 (available with the online version of this paper). An approximately 3.2 kb region containing the p42 mpl gene (MYPE6630) and its invertible promoter region (see Figs 1a
and 5a
) was amplified from M. penetrans HF-2 genomic DNA by PCR with primers p42-F and p42-R. To minimize mutations caused by PCR amplification, a high-fidelity DNA polymerase (PyroBest; TaKaRa) was used. The corresponding region of the p35 mpl gene (MYPE6810) was also amplified from M. penetrans HF-2 by PCR with primers p35-F and p35-R. The amplified p42 and p35 regions were inserted into the pENTR/D-TOPO plasmid by using the TOPO cloning system according to the manufacturer's instructions (Invitrogen), resulting in plasmids pAH501 and pAH502 (Table 1
). The cloned p42 and p35 promoter sequences on these plasmids were in the ON direction. To introduce the p42 promoter sequence into M. pneumoniae cells, the cloned p42 region on plasmid pAH501 was transferred to the SmaI site of the Tn4001mod vector plasmid pISM2062.2 (Knudtson & Minion, 1993
) by using the Gateway cloning technique (Invitrogen). Briefly, pISM2062.2 was converted into the Gateway destination vector by inserting the Gateway vector conversion system (reading frame cassette A) at the SmaI site. The p42 sequence of the pAH501 plasmid was transferred to the pISM2062.2 destination vector by the LR reaction of the Gateway system. The resulting plasmid was designated pAH511 (Table 1
) and introduced into M. pneumoniae M129 by electroporation. The p42 and p35 promoter sequences on the pAH501 and pAH502 plasmids, respectively, were also transferred to the SmaI site of the pCL1920 plasmid, which has a pSC101 replicon (Lerner & Inouye, 1990
), by using the Gateway cloning system for introduction into E. coli cells. These plasmids were designated pAH521 and pAH522, respectively (Table 1
).
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Protein analysis.
E. coli BL21(DE3) strains harbouring plasmids pAH331mut, pAH332mut or pColdI were grown at 37 °C until the mid-exponential phase. The cultures were maintained at 15 °C for 30 min, and 0.2 mM final concentration of IPTG was added. After the addition of IPTG, the cultures were maintained at 15 °C with shaking for 24 h. E. coli cells were collected from a 1 ml volume of the cultures by centrifugation at 20 000 g for 2 min and lysed by adding 150 µl of a sample loading buffer for SDS-PAGE. The samples were then subjected to SDS-PAGE at a load of 15 µl per lane. The proteins were visualized by Coomassie brilliant blue staining. For Western blot analysis, the proteins, separated by SDS-PAGE, were transferred onto a nitrocellulose membrane (Bio-Rad). Monoclonal antibody specific for His6-tag (Cell Signaling Technology) was used at a 1 : 1000 dilution to detect His6-tagged MYPE2900 and MYPE8180 proteins. The reacting antibodies were detected with an alkaline phosphatase-conjugated secondary antibody (goat anti-mouse immunoglobulin G; Promega) and 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium (BCIP/NBT) Colour Development Substrate (Promega) according to the manufacturer's instructions.
PCR detection of mpl gene promoter inversion.
The PCR primer sets designed for the detection of inversions of the mpl gene promoters are listed in Supplementary Table S2. Each primer set consists of three primers [promoter (P), forward (F) and reverse (R) primers]. Two PCRs were performed using these primer sets (with FP primers or RP primers) for each of the corresponding mpl gene promoters to detect the inversion event (see Figs 1
and 5
). Genomic DNAs from M. penetrans HF-2 or M. pneumoniae M129-p42 were analysed with this PCR. The E. coli plasmid DNAs carrying the p42 or p35 promoter regions were also analysed with this method. Genomic DNAs of M. pneumoniae M129-p42 transformants were extracted from 25 ml of culture by the QIAamp mini kit. The genomic DNAs were diluted and 1 ng of each (about 1x106 copies of M. pneumoniae M129 genome) was examined by PCR. For purification of M. penetrans HF-2 genomic DNA, a single colony of M. penetrans HF-2 on a PPLO agar plate [derived from the same culture stock used for genome sequencing (Sasaki et al., 2002
)] was picked up and cultured in 2 ml PPLO liquid medium at 37 °C. After growth, 100 µl of the culture was added to 25 ml fresh PPLO liquid medium and cultured until the medium colour changed to orange. Genomic DNA was extracted from 1 ml of the culture by the QIAamp mini kit. One nanogram of the purified genomic DNA (about 6x105 copies of M. penetrans HF-2 genome) was subjected to the PCR analysis. E. coli plasmid DNAs were extracted from 4 ml of the E. coli cultures by the QIAprep Spin Miniprep kit (Qiagen). One microlitre of plasmid solution was subjected to PCR examination. The PCR mixture Premix Ex Taq Hot Start Version (TaKaRa) was used for the PCR examination, and the PCR was performed under the following conditions: 30 cycles of 98 °C for 10 s, 55 °C for 30 s, and 72 °C for 2.5 min. The PCR products were analysed by 0.8 % (w/v) agarose gel electrophoresis and visualized by ethidium bromide staining. For sequencing analysis, the PCR products were excised from agarose gels and extracted by using the MinElute gel extraction kit (Qiagen). The extracted DNAs were sequenced by the dye-termination method by using corresponding P, F, or R primers and an ABI PRISM 3130xl Genetic Analyzer (Applied Biosystems).
| RESULTS |
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We then introduced recombinase genes into the M129-p42 cells. The MYPE2900 and MYPE8180 clones linked with M. pneumoniae Ptuf promoter were introduced into M129-p42 cells by using the Tn4001mod derivative vector that carries a CmR marker (see Methods). Thus transformants of M129-p42 (GmR-CmR) having the p42 promoter sequence and the recombinase genes were obtained. We then extracted genomic DNA from these transformants (whole transformed population) and examined the direction of the p42 promoter by PCR. This analysis showed that both 2 and 1.2 kb products were amplified from the genomic DNA carrying the MYPE2900 gene (Fig. 1b
, lanes 1 and 2). However, only 2 kb product was obtained from the genomic DNAs carrying the MYPE8180 gene (Fig. 1b
, lanes 3 and 4) or Tn4001mod vector alone (Fig. 1b
, lanes 5 and 6). These results suggested that the MYPE2900 protein is the recombinase that has an activity to invert the p42 promoter sequence.
Reconstruction of the mpl promoter inversion system in E. coli
To further characterize mpl promoter inversion and to develop a simple experimental system, we reconstructed the mpl promoter inversion system in E. coli. Similar to standard mycoplasmal genes, MYPE2900 and MYPE8180 have UGA codons, which are translated into tryptophan in mycoplasma cells. MYPE2900 has a single UGA codon, and MYPE8180 has two UGA codons. Since these UGA codons block full translation of MYPE2900 and MYPE8180 in E. coli, we converted these UGA codons into UGG. The converted MYPE2900 and MYPE8180 genes (MYPE2900mut and MYPE8180mut) were linked with the E. coli cspA promoter and His6-tag sequence at the 5' end on plasmid pAH331mut and pAH332mut, respectively (see Methods and Table 1
). Plasmids pAH331mut and pAH332mut were introduced into E. coli BL21(DE3), and the strain was cultured under appropriate conditions to activate the cspA promoter (see Methods). After 24 h culture at 15 °C with or without IPTG, the expression of MYPE2900 and MYPE8180 proteins was detected by immunoblot analysis specific for His6-tag (Fig. 2
). The MYPE2900 and MYPE8180 proteins were produced apparently in the presence of IPTG (Fig. 2
, lanes 10 and 12), although the reason for the low expression level of MYPE8180 compared to MYPE2900 is not clear. In addition, a weak expression of MYPE2900 was observed in the absence of IPTG (Fig. 2
, lane 9).
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| DISCUSSION |
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In our previous study, we did not perform direct detection of mpl promoter inversions in M. penetrans cells (Horino et al., 2003
). In the present study, we used a PCR-based method and found the presence of an inverted form of 10 mpl gene promoters (including the p35 and p42 promoters) in M. penetrans genomic DNA. Inversions of these mpl gene promoters occurred at the 12 bp IR sequences that are similar to those of the p35 and p42 promoters (Fig. 4b
), suggesting that all these promoter inversions may be catalysed by MYPE2900 recombinase in M. penetrans cells. The 12 bp IR sequences of all mpl genes slightly differ from each other and show the consensus sequence TAAYNNNDATTA. This type of dyad motif is commonly present as a recognition site of site-specific DNA recombinases. However, the 12 bp sequence is considerably shorter than that of the other known recombination sites recognized by site-specific DNA recombinases (Glew et al., 2002
; Honarvar et al., 2003
; Li et al., 2002
; Lysnyansky et al., 2001
; Sitaraman et al., 2002
). The variation in 12 bp IRs of the mpl gene promoters may contribute to the prevention of inappropriate recombination between different mpl gene promoters and to maintaining the structure of the mpl gene cluster (Fig. 5a
). The variation in recombination sites may also affect the frequency of inversion of individual promoters. In this study, we did not examine the inversion frequency of each promoter. This could be evaluated by a real-time PCR method or by using reconstruction systems in M. pneumoniae and E. coli cells in further studies.
Another characteristic feature of the mpl promoter inversion system is the location of the recombinase gene. In many site-specific recombination systems, which control antigenic variations, the Tsr family genes tend to be located near the recombination sites (Chopra-Dewasthaly et al., 2008
; Komano, 1999
; Kuwahara et al., 2004
; Ron et al., 2002
). However, in the mpl promoter inversion system, the MYPE2900 gene is located approximately 500 kb apart from the major mpl gene cluster. The other two minor mpl gene clusters are also separated by approximately 600 or 40 kb from the MYPE2900 gene (Horino et al., 2003
). In addition, MYPE2900 recombinase efficiently catalysed the inversions of the p42 and p35 promoters in a trans-acting manner in E. coli cells (the MYPE2900 gene and the p42 or p35 promoters were present in different plasmids). Probably, there is no cis-acting effect between the MYPE2900 gene and mpl promoter recombination sites.
The amino acid sequence of MYPE8180 strongly suggests that it is also a Tsr. However, in our experimental conditions, the MYPE8180 product did not show recombinase activity in p42 and p35 promoter inversions. The reconstruction systems in this study are not identical to the natural context in M. penetrans cells, so that there are still possibilities that MYPE8180 recombinase takes part in the mpl system with additional factors in M. penetrans cells or that the His6-tag fused to MYPE8180 in this study disturbed the recombinase activity. However, it is also possible that MYPE8180 has no activity in mpl promoter inversions, but is involved in another site-specific recombination system of the M. penetrans genome. It is known that several mycoplasma species such as Mycoplasma genitalium and M. pneumoniae lack xer-like site-specific recombinase genes, possibly because of reductive evolution of their minimum genomes (approx. 580 and 816 kb in size) (Himmelreich et al., 1997
). This fact suggests that these mycoplasma species, as a result of reductive evolution, do not require Xer-like recombinase for resolving their dimer chromosomes during cell division (Glew et al., 2002
; Recchia & Sherratt, 1999
). However, the genome of M. penetrans (1.36 Mb) is approximately twice as large as that of these species. Furthermore, MYPE8180 shows strong homology to the XerC/D group of the Tsr family proteins. Thus, there is a possibility that MYPE8180 is involved in a Xer-like site-specific recombination system for chromosome segregation in M. penetrans. There is a further possibility that MYPE8180 is involved in another phase or antigenic variation system. To examine these possibilities, identification of the target sequence of MYPE8180 would be an interesting future study.
Identification of MYPE2900 recombinase in this study may lead to further research on disruption of the MYPE2900 gene and development of phase-variation-deficient (phase-locked) strains of M. penetrans. Such phase-locked strains were recently developed in M. agalactiae, a ruminant pathogen that has a multiple site-specific recombination system responsible for its surface lipoprotein variation (Chopra-Dewasthaly et al., 2008
). Phase-locked strains are useful for investigating host–pathogen interactions and for determining the functions of each lipoprotein variant. Although a gene disruption method needs to be developed in M. penetrans, an MYPE2900-deficient mutant might be developed in future studies. These attempts may provide an insight into the extent to which surface antigenic variations of mycoplasmas are involved in host immune evasion and help to establish their parasitic lifestyle. An understanding of these pathogenic mechanisms of mycoplasmas may be helpful for designing strategies to eradicate chronic mycoplasma infection.
| ACKNOWLEDGEMENTS |
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Edited by: C. Citti
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Received 27 October 2008;
revised 6 January 2009;
accepted 8 January 2009.
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